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Fluent genomic data analysis with plyranges

Instructor(s) name(s) and contact information

Stuart Lee - lee.s at wehi.edu.au

Michael Lawrence - lawremi at gmail

Workshop Description

In this workshop, we will give an overview of how to perform low-level analyses of genomic data using the grammar of genomic data transformation defined in the plyranges package. We will cover:

  • introduction to GRanges
  • overview of the core verbs for arithmetic, restriction, and aggregation of GRanges objects
  • performing joins between GRanges objects
  • using the above to perform coverage analysis

The workshop will be a computer lab, in which the participants will be able to ask questions and interact with the instructors.

Pre-requisites

This workshop is mostly self-contained however familiarity with the following would be useful:

  • plyranges vignette
  • the GenomicRanges and IRanges packages
  • tidyverse approaches to data analysis

Workshop Participation

Students will work through an Rmarkdown document while the instructors respond to any questions they have.

R / Bioconductor packages used

  • plyranges
  • HelloRanges

Time outline

Activity Time
Introduction and plan 10m
Basic wrangling 20m
Coverage analysis 20m

Workshop goals and objectives

Learning goals

  • Understand that GRanges follows tidy data principles
  • Apply the plyranges grammar to genomic data analysis

Learning objectives

  • Read files into R as GRanges objects
  • Perform coverage analysis
  • Build data pipelines for analysis based on GRanges
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